A comprehensive Model Context Protocol server for accessing Protein Data Bank (PDB) with 28 structural biology tools for protein structure analysis
A comprehensive Model Context Protocol server for accessing Protein Data Bank (PDB) with 28 structural biology tools for protein structure analysis, validation, and comparison. That is what the pdb mcp server brings to an AI assistant: the same capability, reachable through the Model Context Protocol rather than a separate app or dashboard.
A Model Context Protocol (MCP) server that provides access to the Protein Data Bank (PDB) - the worldwide repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.
The server publishes 7 tools. What each one is for:
search_structures — Search PDB database for protein structures by keyword, protein name, or PDB IDget_structure_info — Get detailed information for a specific PDB structuredownload_structure — Download structure coordinates in various formats (PDB, mmCIF, mmTF, XML)search_by_uniprot — Find PDB structures associated with a UniProt accessionget_structure_quality — Get structure quality metrics and validation dataTools — The Tools tool exposed by this serverResources — The Resources tool exposed by this serverThe server ships on npm as npm, so your MCP client can launch it on demand — there is no separate build step. Add the server block to your client's configuration, restart it, and the tools register themselves.
Among the database access options, the useful question is rarely "what can it do" but "what does it cost you to run" — permissions, credentials, and how much of your context its toolset consumes. PDB's toolset — search_structures, get_structure_info, download_structure and 4 more — is a fair guide to whether it matches your workflow. It is maintained by Augmented-Nature; worth a glance at recent repository activity before you build anything load-bearing on it.
This entry was verified against PDB's own documentation before publication; SyncDev keeps the directory reviewed rather than auto-generated.
| Tool | What it does |
|---|---|
| search_structures | Search PDB database for protein structures by keyword, protein name, or PDB ID |
| get_structure_info | Get detailed information for a specific PDB structure |
| download_structure | Download structure coordinates in various formats (PDB, mmCIF, mmTF, XML) |
| search_by_uniprot | Find PDB structures associated with a UniProt accession |
| get_structure_quality | Get structure quality metrics and validation data |
| Tools | The Tools tool exposed by this server. |
| Resources | The Resources tool exposed by this server. |
{
"mcpServers": {
"pdb": {
"command": "npx",
"args": ["-y", "npm"]
}
}
}Add to claude_desktop_config.json, then restart Claude Desktop.
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